LAMMPS (30 Jul 2021) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98) using 1 OpenMP thread(s) per MPI task Lattice spacing in x,y,z = 3.4986963 3.4986963 3.4986963 Created orthogonal box = (0.0000000 -70.152142 0.0000000) to (40.500338 70.152142 6.0599198) 1 by 1 by 1 MPI processor grid Lattice spacing in x,y,z = 5.4403439 5.5839716 6.0599198 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.152142 0.0000000) to (40.500338 70.152142 6.0599198) create_atoms CPU = 0.010 seconds 1610 atoms in group upper Displacing atoms ... Lattice spacing in x,y,z = 5.4403439 5.5839716 6.0599198 Created 1610 atoms using lattice units in orthogonal box = (0.0000000 -70.152142 0.0000000) to (40.500338 70.152142 6.0599198) create_atoms CPU = 0.010 seconds 1610 atoms in group lower Displacing atoms ... System init for delete_atoms ... Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 2 neighbor lists, perpetual/occasional/extra = 1 1 0 (1) command delete_atoms, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Deleted 36 atoms, new total = 3184 CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE Your simulation uses code contributions which should be cited: - OpenKIM: https://doi.org/10.1007/s11837-011-0102-6 - OpenKIM potential: https://openkim.org/cite/MO_715003088863_000#item-citation The log file lists these citations in BibTeX format. CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 0 Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13024.573 0 -13024.573 1439.8894 87 0 -13069.868 0 -13069.868 -8721.8267 Loop time of 9.54183 on 1 procs for 87 steps with 3184 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13024.5734373152 -13069.8566027462 -13069.8681396448 Force two-norm initial, final = 31.844947 0.35019239 Force max component initial, final = 6.5006175 0.057001137 Final line search alpha, max atom move = 0.89933815 0.051263297 Iterations, force evaluations = 87 152 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 9.1199 | 9.1199 | 9.1199 | 0.0 | 95.58 Neigh | 0.31354 | 0.31354 | 0.31354 | 0.0 | 3.29 Comm | 0.057542 | 0.057542 | 0.057542 | 0.0 | 0.60 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.05086 | | | 0.53 Nlocal: 3184.00 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14166.0 ave 14166 max 14166 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556372.0 ave 556372 max 556372 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556372 Ave neighs/atom = 174.73995 Neighbor list builds = 4 Dangerous builds = 0 WARNING: Using 'neigh_modify every 1 delay 0 check yes' setting during minimization (src/min.cpp:189) Neighbor list info ... update every 1 steps, delay 0 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 1 neighbor lists, perpetual/occasional/extra = 1 0 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard Setting up cg style minimization ... Unit style : metal Current step : 87 WARNING: Energy due to 3 extra global DOFs will be included in minimizer energies Per MPI rank memory allocation (min/avg/max) = 10.95 | 10.95 | 10.95 Mbytes Step Temp E_pair E_mol TotEng Press Volume 87 0 -13069.868 0 -13069.868 -8721.8267 34434.713 91 0 -13070.239 0 -13070.239 -3370.3717 34272.597 Loop time of 0.360914 on 1 procs for 4 steps with 3184 atoms 100.1% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = -13069.8681396449 -13070.2351933105 -13070.2388008572 Force two-norm initial, final = 205.96595 2.9259875 Force max component initial, final = 179.84211 2.8365004 Final line search alpha, max atom move = 5.4601874e-05 0.00015487824 Iterations, force evaluations = 4 5 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.35256 | 0.35256 | 0.35256 | 0.0 | 97.68 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0.0018445 | 0.0018445 | 0.0018445 | 0.0 | 0.51 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.006511 | | | 1.80 Nlocal: 3184.00 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14008.0 ave 14008 max 14008 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556460.0 ave 556460 max 556460 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556460 Ave neighs/atom = 174.76759 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes Step Temp E_pair E_mol TotEng Press 0 0 -13070.239 0 -13070.239 -3370.3717 Loop time of 6.946e-06 on 1 procs for 0 steps with 3184 atoms 187.2% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 6.946e-06 | | |100.00 Nlocal: 3184.00 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14073.0 ave 14073 max 14073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 0.00000 ave 0 max 0 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556716.0 ave 556716 max 556716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556716 Ave neighs/atom = 174.84799 Neighbor list builds = 0 Dangerous builds = 0 Neighbor list info ... update every 1 steps, delay 10 steps, check yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 7.6 ghost atom cutoff = 7.6 binsize = 3.8, bins = 11 37 2 3 neighbor lists, perpetual/occasional/extra = 1 2 0 (1) pair kim, perpetual attributes: full, newton off, cut 7.6 pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (2) compute centro/atom, occasional attributes: full, newton on pair build: full/bin/atomonly stencil: full/bin/3d bin: standard (3) compute pair/local, occasional attributes: half, newton on pair build: half/bin/atomonly/newton stencil: half/bin/3d bin: standard Setting up Verlet run ... Unit style : metal Current step : 0 Time step : 0.001 Per MPI rank memory allocation (min/avg/max) = 10.46 | 10.46 | 10.46 Mbytes Step v_pe_metal c_particle_engsum v_lx_metal v_ly_metal v_lz_metal Press v_press_metal v_pxx_metal v_pyy_metal v_pzz_metal v_mindist_metal v_csymsum_metal 0 -13070.239 -13070.239 40.363433 140.30428 6.0518477 -3370.3717 -3370.3717 20.407583 -10263.947 132.42418 2.2302807 1283.8377 Loop time of 7.027e-06 on 1 procs for 0 steps with 3184 atoms 284.6% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0 | 0 | 0 | 0.0 | 0.00 Neigh | 0 | 0 | 0 | 0.0 | 0.00 Comm | 0 | 0 | 0 | 0.0 | 0.00 Output | 0 | 0 | 0 | 0.0 | 0.00 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 7.027e-06 | | |100.00 Nlocal: 3184.00 ave 3184 max 3184 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 14073.0 ave 14073 max 14073 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 278358.0 ave 278358 max 278358 min Histogram: 1 0 0 0 0 0 0 0 0 0 FullNghs: 556716.0 ave 556716 max 556716 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 556716 Ave neighs/atom = 174.84799 Neighbor list builds = 0 Dangerous builds = 0 3184 -13070.2388008572 eV 2.23028070575466 Angstroms This indicates that LAMMPS ran successfully Total wall time: 0:00:11